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Wario's Woods isn't the most memorable game on the NES, but it was important for giving Mario's rival a foundation to get his own series of games. In Wario's Woods, players would be competing in a puzzle format
to defeat a host of characters from the Super Mario franchise.
With Dr. Mario being the only big puzzle game represented on the NES Classic, omitting such an important character from it seems like an odd choice. Wario has a long history with Nintendo and is more than just a spin-off character. By all means, he should've been on the NES Classic.